Your problem is coming from the non amplified speakers. You wont need to do this. As others said, check your HU's ground. If it didnt happen with the stock unit, then your issue is either a noisy HU or you have a weak connection at your ground wire on the HU. A real quick test, just run your own ground wire, connect it and see if the alt noise goes away. If it doesnt, plug your stock HU back in and if it's gone, your new HU has problems.
If that were the case, you'd run into the same issue with the stock unit.